ABSTRACT: Pygmy seahorses are a group of little-known miniature hippocampid fish that differ considerably in biology and ecology from their larger congeners. We estimated the population density, sex ratio and habitat of 2 sympatric, obligate gorgonian-associated pygmy seahorses, Hippocampus bargibanti and H. denise, in a 20 km long coastal marine protected area in southeast Sulawesi, Indonesia. Belt transects covering 200 m² each were surveyed at 7 sites and 5 depth contours to record the density of seahorses and their host gorgonians. The population density (±SE) was 1.17 (±0.27) per 200 m² for H. denise and 0.34 (±0.20) per 200 m² for H. bargibanti, some of the lowest densities for unexploited seahorse populations studied thus far. Male−female pairs (43.9%) were the most common group composition for H. denise, with single, 3 or 4 individuals found on 19.5, 7.3 and 29.3% of inhabited gorgonians, respectively. H. denise inhabited 7.8% of Annella reticulata gorgonians within the survey area but were recorded from a total of 8 gorgonian genera during extensive opportunistic ad hoc searches. Annella spp. density was 10.7 times higher than that of Muricella spp. (the sole host of H. bargibanti), of which 20.0% were inhabited. The small population size, occurrence of pygmy seahorses in groups on their hosts with the resulting skew in sex ratios, and habitat specialisation likely all impact the ­species’ population dynamics, and hence these need to be considered in conservation management strategies.